SINH THÁI HỌC PHÂN TỬ: MỘT SỐ VẤN ĐỀ LÝ THUYẾT VÀ ỨNG DỤNG THỰC TIỄN
Nội dung chính của bài viết
Tóm tắt
MOLECULAR ECOLOGY: SOME THEORETICAL CHALLENGES AND APPLICATIONS
With the development of molecular marker technology in the 1980s, specially their applications solving basic questions and ecological research. To explore the knowledge about molecular ecology, several reviews have been published in the sincelast three decades. The molecular markers have been widely used in study and selection of plants and animals. Molecular marker used in studies of genetic diversity, phylogeny, classification, gene tagging and identification; in germplasm and marker assisted selection. The presence of various types of molecular marker, and differences in their principles, methodologies, and applications require careful consideration in choosing one or more of such methods. Meanwhile, no molecular markeris available that fulfill all requirements needed by researchers. Depending on the nature of each study, one can choose among the variety of molecular marker techniques, each of which combines at least some desirable properties. However, all these reviews were meant for researchers with advanced knowledge of molecular genetics (gene identification and gene mapping), genetic diversity and structure of population, phylogenetic relationship and breeding (plant and animal). This review will provide better understanding in science and technology about recent developments in molecular markers, their applications and possibly devoted to early researchers with a little or no knowledge of molecular markers.
Từ khóa
Molecular marker, chỉ thị phân tử, sinh thái, ứng dụng
Chi tiết bài viết
Tài liệu tham khảo
1. Nadeem M.A., Nawaz M.A., Shahid M.Q, Dogan Y., Comertpay G., Yıldız M., Hatipoglu R., Ahmad F., Alsaleh A., Labhane N., Ozkan H., Chung G., Baloch F.S., DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing, Biotechnology & Biotechnological Equipment, 2018, 32(2):261-285.
2. Johnson J.B., Peat, S.M., Adams B.J., Where's the ecology in molecular ecology? Oikos, 2009, 118(11):1601-1609.
3. Ricklefs R.E., Miller, G.L., Ecology. - W. H. Freeman, 1999.
4. Futuyma D.J., Evolution, Sinauer & Associates." Inc., Sunderland, Massachusetts, 2005, p.226-243.
5. Charlesworth B., Measures of divergence between populations and the effect of forces that reduce variability, Mol. Biol. Evol, 1998, 15:538-543.
6. Grant W.S., Molecular ecology and evolution: Approaches and applications, Journal of Experimental Marine Biology and Ecology, 1995, 191(1):119-121.
7. Nguyễn Đức Thành, Các kỹ thuật chỉ thị DNA trong nghiên cứu và chọn lọc thực vật, Tạp chí Sinh học, 2014, 36(3):265-294.
8. Williams J.G.K., Kubelik A.R., Livak K.J., Rafalski J.A., Tingey S.V., DNA polymorphisms amplified by arbitrary primers are useful as genetic markers.
Nucleic Acids Res., 1990, 18:6531-6535.
9. Adams M.D., Kelley J.M., Gocayne J.D., Dubrick M., Complementary DNA sequencing: expressed sequence tags and human genome project, Science 252, 1991, p.1651-1656.
10. Akkaya M.S., Bhagwat A.A., Cregan P.B., Length polymorphisms of simple sequence repeat DNA in soybean, Genetics, 1992, 132:1131-1139.
11. Jordan S.A., Humphries P., Single nucleotide polymorphism in exon 2 of the BCP gene on 7q31-q35, Hum. Mol. Genet., 1994, 3:1915.
12. Zietkiewicz E., Rafalski A., Labuda D., Genome fingerprinting by simple sequence repeats (SSR)-anchored PCR amplification, Genomics, 1994, 20:176-183.
13. Vu Thi Thu Hien, Dinh Thi Phong, Genetic diversity among endangered rare Dalbergia cochinchinensis (Fabaceae) genotypes in Vietnam revealed by random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) markers, Afri J Biotechnol, 2012, 11(35):8632-8644.
14. Nguyen Minh Tam, Vu Dinh Duy, Nguyen Minh Duc, Preserve of threatened conifers (Cupressaceae) in Vietnam, Curr Res J Biol Sci, 2013, 5(4):141-148.
15. Nguyen Minh Tam, Vu Dinh Duy, Nguyen Minh Duc, Vu Dinh Giap, Genetic diversity in the natural populations of Dipterocarpus costatus
(Dipterocarpaceae), Res J Biotechnol., 2014, 9(8):14-19.
16. Dinh Thi Phong, Vu Thi Thu Hien, Tran Thi Lieu, Nguyen Tien Hiep, Genetic diversity in the natural populations of Pinus dalatensis Ferre’ (Pinaceae) assessed by SSR markers. Journal of Science and Technology, 2016, 54(2):178-189
17. Trang N.T.P., Triest L., Genetic structure of the threatened Hopea chinensis in the Quang Ninh province, Vietnam, Genet Mol Res, 2016, 15(2):1-13.
18. Dinh Duy Vu, Thi Tuyet Xuan Bui, Minh Tam Nguyen, Dinh Giap Vu, Minh Duc Nguyen, Van Thang Bui, Xiaohua Huang, Yi Zhang, Genetic diversity in two threatened species in Viet Nam: Taxus chinensis and Taxus wallichiana, Journal of Forestry Research, 2017, 28(2):265-272.
19. Dinh Duy Vu, Thi Tuyet Xuan Bui, Minh Duc Nguyen, Syed Noor Muhammad Sha, Dinh Giap Vu, Yi Zhang, Minh Tam Nguyen, Xiao Hua Huang, Genetic diversity and conservation implication of the threatened dipterocarps (Dipterocarpaceae) in southeast Vietnam. Journal of Forestry Research, 2018, https://doi.org/10.1007/s11676-018-0735-1. First Online: 02 July 2018.
20. Nguyen Duc Thanh, Nguyen Thi Kim Lien, Pham Quang Chung, Tran Quoc Trong, Le Thi Bich Thuy, Henry Nguyen, Mapping QTLs associated with root traits related to drought resistance in Vietnamese upland rice, Asean Journal on Sci. & Tech. for Development (AJSTD), 2006, 23(4):323-332.
21. Nguyen Thi Lang, Bui Chi Buu, Fine mapping for drought tolerance in rice (Oryza sativa L.), Omonrice, 2008, 16:9-15.
22. Nguyen Thi Lang, Nguyen Van Tao, Bui Chi Buu, Marker-assisted backcrossing (MAB) for rice submergence tolerance in Mekong Delta. Omonrice, 2011, 18:11-21.
23. Nguyễn Thị Kim Liên, Nông Văn Hải, Nguyễn Đức Thành, Kết quả bước đầu của việc ứng dụng chỉ thị SSR trong chọn dòng chịu hạn ở lúa cạn, Báo cáo Khoa học, Hội nghị Công nghệ sinh học toàn quốc, Hà Nội, 2003, tr. 898-901.
24. Beebee T., Rowe G., An Introduction to Molecular Ecology, 2nd ed. New York, NY: Oxford University Press, 2008.
25. Behura S.K., Molecular Marker Systems in Insects: Current Trends and Future Avenues, Molecular Ecology, 2006, 15:3087-3113.
26. Monsen-Collar K.J., Dolcemascolo P., Using Molecular Techniques to Answer Ecological Questions, Nature Education Knowledge, 2010, 3(10):1.
27. Wilson M.J., Weightman A.J., Wade W.G., Applications of molecular ecology in the characterization of uncultured microorganisms associated with human disease, Reviews in medical microbiology, 1997, 8(2):91-10.
28. Christiansen D.G., Reyer H.U., Effects of geographic distance, sea barriers and habitat on the genetic structure and diversity of all-hybrid water frog populations. Heredity, 2011, 106:25-36.
29. Huang H., Wang H., Li L., Wu Z., Chen J., Genetic diversity and population demography of the Chinese crocodile lizard (Shinisaurus crocodilurus) in China, PLoS ONE, 2014, 9(3):e91570.
30. Hoffmann A., Plötner J., Pruvost N.B.M., Christiansen D.G., Röthlisberger S., Choleva L., Mikulíček P., Cogălniceanu D., SasKovács I., Shabanov D., MorozovLeonov S., Reyer H, Genetic diversity and distribution patterns of diploid and polyploid hybrid water frog populations (Pelophylax esculentus complex) across Europe, Molecular Ecology, 2015, 24:4371-4391.
31. Pepper M., Hamilton D.G., Merkling T., Svedin N., Cser B., Catullo R.A., Pryke S.R., Keogh J.S., Phylogeographic structure across one of the largest intact tropical savannahs: Molecular and morphological analysis of Australia’s iconic frilled lizard Chlamydosaurus kingie, Molecular Phylogenetics and Evolution, 2017, 106:217-227.
32. Lebas N., Spencer P.B.S., Polymorphic microsatellite markers in the ornate dragon lizard, Ctenophorus ornatus, Molecular Ecology, 2000, 9:365-378.
33. Gao J., Qiye L.Q., Wang Z., Zhou Y., Martelli P., Li F., Xiong Z., Wang J., Yang H., Zhang G., Sequencing, de novo assembling, and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus, Gigascience, 2017, 6:1-6.
34. Frere C.H., Prentis P.J., Ezaz T., Georges A., Isolation and characterisation of novel microsatellite and mitochondrial DNA markers for the Eastern Water Dragon (Physignathus lesueurii), Conservation Genet Resour, 2012, 4:113-116.
35. Melville J., Shoo L.P., Doughty P., Phylogenetic relationships of the heath dragons (Rankinia adelaidensis and R. parviceps) from the south-western Australian biodiversity hotspot, Australian Journal of Zoology, 2008, 56:159-171.
36. Amer SAM, Kumazawa Y, The mitochondrial genome of the lizard Calotes versicolor and a novel gene inversion in South Asian Draconine Agamids, Mol. Biol. Evol, 2007, 24(6):1330-1339.
37. Ujvari B., Dowton M., Madsen T., Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii), Molecular Ecology, 2008, 17:3557-3564.
38. Nguyen T.T., Matsui M., Eto K., Nikolai Orlov N., A preliminary study of phylogenetic relationships and taxonomic problems of Vietnamese Rhacophorus (Anura: Rhacophoridae). Russian Journal of Herpetology, 2014, 21(4):274-280
39. Nguyen T.T., Matsui M., Eto K., Mitochondrial phylogeny of an Asian tree frog genus Theloderma (Anura: Rhacophoridae), Molecular Phylogenetics and Evolution, 2015, 85:59-67.
40. Takeuchi H., Savitzky A.H., Ding L., Silva A.D., Das I., Nguyen T.T., Tsai T.S., Jono T., Zhu G.X., Mahaulpatha D., Tang Y., Mori A., Evolution of nuchal glands, unusual defensive organs of Asian natricine snakes (Serpentes: Colubridae), inferred from a molecular phylogeny, Ecology and Evolution. 2018, p.1-14.
41. Nguyễn Thị Thắm, Ngô Thị Hạnh, Nguyễn Quảng Trường, Thomas Ziegler, Mona Van Schingen, Nguyễn Thị Hồng Vân, Lê Đức Minh, Sử dụng chỉ thị Microsatellite trong nghiên cứu quần thể loài thằn lằn cá sấu (Shinisaurus crocodilurus Ahl, 1930) tại Việt Nam, Tạp chí Khoa học ĐHQGHN: Các Khoa học Trái đất và Môi trường, 2017, 33(1S):100-108.
42. Wei X.X., Yang Z.Y., Li Y., Wang X.Q., Molecular phylogeny and biogeography of Pseudotsuga (Pinaceae): Insights into the floristic relationship between Taiwan and its adjacent areas, Molecular Phylogenetics and Evolution, 2010, 55:776-785.
43. Tamaki S., Isoda K., Takahashi M., Yamada Y., Yamashita Y., Genetic structure and diversity in relation to the recently reduced population size of the rare conifer, Pseudotsuga japonica, endemic to Japan, Conservation Genetics, 2018, 19(5):1243-1255
44. Castelán P.M., Cruz M.C., Castillo M.C.M., Izquierdo S.C., Upton J.L., Padilla IS., Cruz V.G., Diversity and genetic structure inferred with microsatellites in natural populations of Pseudotsuga menziesii (Mirb.) Franco (Pinaceae) in the central region of Mexico, Forests, 2019, 10:101.
45. Ho C.S., Shih H.C., Liu H.Y., Chiu S.T., Chen M.H., Ju L.P., KoY.Z., Shih Y.S., Chen C.T., Hsu T.W., Chiang Y.C., Development and characterization of 16 polymorphic microsatellite markers from Taiwan cow-tail fir, Keteleeria davidiana var. formosana (Pinaceae) and cross-species amplification in other Keteleeria taxa, BMC Research Notes, 2014, 7:255.
2. Johnson J.B., Peat, S.M., Adams B.J., Where's the ecology in molecular ecology? Oikos, 2009, 118(11):1601-1609.
3. Ricklefs R.E., Miller, G.L., Ecology. - W. H. Freeman, 1999.
4. Futuyma D.J., Evolution, Sinauer & Associates." Inc., Sunderland, Massachusetts, 2005, p.226-243.
5. Charlesworth B., Measures of divergence between populations and the effect of forces that reduce variability, Mol. Biol. Evol, 1998, 15:538-543.
6. Grant W.S., Molecular ecology and evolution: Approaches and applications, Journal of Experimental Marine Biology and Ecology, 1995, 191(1):119-121.
7. Nguyễn Đức Thành, Các kỹ thuật chỉ thị DNA trong nghiên cứu và chọn lọc thực vật, Tạp chí Sinh học, 2014, 36(3):265-294.
8. Williams J.G.K., Kubelik A.R., Livak K.J., Rafalski J.A., Tingey S.V., DNA polymorphisms amplified by arbitrary primers are useful as genetic markers.
Nucleic Acids Res., 1990, 18:6531-6535.
9. Adams M.D., Kelley J.M., Gocayne J.D., Dubrick M., Complementary DNA sequencing: expressed sequence tags and human genome project, Science 252, 1991, p.1651-1656.
10. Akkaya M.S., Bhagwat A.A., Cregan P.B., Length polymorphisms of simple sequence repeat DNA in soybean, Genetics, 1992, 132:1131-1139.
11. Jordan S.A., Humphries P., Single nucleotide polymorphism in exon 2 of the BCP gene on 7q31-q35, Hum. Mol. Genet., 1994, 3:1915.
12. Zietkiewicz E., Rafalski A., Labuda D., Genome fingerprinting by simple sequence repeats (SSR)-anchored PCR amplification, Genomics, 1994, 20:176-183.
13. Vu Thi Thu Hien, Dinh Thi Phong, Genetic diversity among endangered rare Dalbergia cochinchinensis (Fabaceae) genotypes in Vietnam revealed by random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) markers, Afri J Biotechnol, 2012, 11(35):8632-8644.
14. Nguyen Minh Tam, Vu Dinh Duy, Nguyen Minh Duc, Preserve of threatened conifers (Cupressaceae) in Vietnam, Curr Res J Biol Sci, 2013, 5(4):141-148.
15. Nguyen Minh Tam, Vu Dinh Duy, Nguyen Minh Duc, Vu Dinh Giap, Genetic diversity in the natural populations of Dipterocarpus costatus
(Dipterocarpaceae), Res J Biotechnol., 2014, 9(8):14-19.
16. Dinh Thi Phong, Vu Thi Thu Hien, Tran Thi Lieu, Nguyen Tien Hiep, Genetic diversity in the natural populations of Pinus dalatensis Ferre’ (Pinaceae) assessed by SSR markers. Journal of Science and Technology, 2016, 54(2):178-189
17. Trang N.T.P., Triest L., Genetic structure of the threatened Hopea chinensis in the Quang Ninh province, Vietnam, Genet Mol Res, 2016, 15(2):1-13.
18. Dinh Duy Vu, Thi Tuyet Xuan Bui, Minh Tam Nguyen, Dinh Giap Vu, Minh Duc Nguyen, Van Thang Bui, Xiaohua Huang, Yi Zhang, Genetic diversity in two threatened species in Viet Nam: Taxus chinensis and Taxus wallichiana, Journal of Forestry Research, 2017, 28(2):265-272.
19. Dinh Duy Vu, Thi Tuyet Xuan Bui, Minh Duc Nguyen, Syed Noor Muhammad Sha, Dinh Giap Vu, Yi Zhang, Minh Tam Nguyen, Xiao Hua Huang, Genetic diversity and conservation implication of the threatened dipterocarps (Dipterocarpaceae) in southeast Vietnam. Journal of Forestry Research, 2018, https://doi.org/10.1007/s11676-018-0735-1. First Online: 02 July 2018.
20. Nguyen Duc Thanh, Nguyen Thi Kim Lien, Pham Quang Chung, Tran Quoc Trong, Le Thi Bich Thuy, Henry Nguyen, Mapping QTLs associated with root traits related to drought resistance in Vietnamese upland rice, Asean Journal on Sci. & Tech. for Development (AJSTD), 2006, 23(4):323-332.
21. Nguyen Thi Lang, Bui Chi Buu, Fine mapping for drought tolerance in rice (Oryza sativa L.), Omonrice, 2008, 16:9-15.
22. Nguyen Thi Lang, Nguyen Van Tao, Bui Chi Buu, Marker-assisted backcrossing (MAB) for rice submergence tolerance in Mekong Delta. Omonrice, 2011, 18:11-21.
23. Nguyễn Thị Kim Liên, Nông Văn Hải, Nguyễn Đức Thành, Kết quả bước đầu của việc ứng dụng chỉ thị SSR trong chọn dòng chịu hạn ở lúa cạn, Báo cáo Khoa học, Hội nghị Công nghệ sinh học toàn quốc, Hà Nội, 2003, tr. 898-901.
24. Beebee T., Rowe G., An Introduction to Molecular Ecology, 2nd ed. New York, NY: Oxford University Press, 2008.
25. Behura S.K., Molecular Marker Systems in Insects: Current Trends and Future Avenues, Molecular Ecology, 2006, 15:3087-3113.
26. Monsen-Collar K.J., Dolcemascolo P., Using Molecular Techniques to Answer Ecological Questions, Nature Education Knowledge, 2010, 3(10):1.
27. Wilson M.J., Weightman A.J., Wade W.G., Applications of molecular ecology in the characterization of uncultured microorganisms associated with human disease, Reviews in medical microbiology, 1997, 8(2):91-10.
28. Christiansen D.G., Reyer H.U., Effects of geographic distance, sea barriers and habitat on the genetic structure and diversity of all-hybrid water frog populations. Heredity, 2011, 106:25-36.
29. Huang H., Wang H., Li L., Wu Z., Chen J., Genetic diversity and population demography of the Chinese crocodile lizard (Shinisaurus crocodilurus) in China, PLoS ONE, 2014, 9(3):e91570.
30. Hoffmann A., Plötner J., Pruvost N.B.M., Christiansen D.G., Röthlisberger S., Choleva L., Mikulíček P., Cogălniceanu D., SasKovács I., Shabanov D., MorozovLeonov S., Reyer H, Genetic diversity and distribution patterns of diploid and polyploid hybrid water frog populations (Pelophylax esculentus complex) across Europe, Molecular Ecology, 2015, 24:4371-4391.
31. Pepper M., Hamilton D.G., Merkling T., Svedin N., Cser B., Catullo R.A., Pryke S.R., Keogh J.S., Phylogeographic structure across one of the largest intact tropical savannahs: Molecular and morphological analysis of Australia’s iconic frilled lizard Chlamydosaurus kingie, Molecular Phylogenetics and Evolution, 2017, 106:217-227.
32. Lebas N., Spencer P.B.S., Polymorphic microsatellite markers in the ornate dragon lizard, Ctenophorus ornatus, Molecular Ecology, 2000, 9:365-378.
33. Gao J., Qiye L.Q., Wang Z., Zhou Y., Martelli P., Li F., Xiong Z., Wang J., Yang H., Zhang G., Sequencing, de novo assembling, and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus, Gigascience, 2017, 6:1-6.
34. Frere C.H., Prentis P.J., Ezaz T., Georges A., Isolation and characterisation of novel microsatellite and mitochondrial DNA markers for the Eastern Water Dragon (Physignathus lesueurii), Conservation Genet Resour, 2012, 4:113-116.
35. Melville J., Shoo L.P., Doughty P., Phylogenetic relationships of the heath dragons (Rankinia adelaidensis and R. parviceps) from the south-western Australian biodiversity hotspot, Australian Journal of Zoology, 2008, 56:159-171.
36. Amer SAM, Kumazawa Y, The mitochondrial genome of the lizard Calotes versicolor and a novel gene inversion in South Asian Draconine Agamids, Mol. Biol. Evol, 2007, 24(6):1330-1339.
37. Ujvari B., Dowton M., Madsen T., Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii), Molecular Ecology, 2008, 17:3557-3564.
38. Nguyen T.T., Matsui M., Eto K., Nikolai Orlov N., A preliminary study of phylogenetic relationships and taxonomic problems of Vietnamese Rhacophorus (Anura: Rhacophoridae). Russian Journal of Herpetology, 2014, 21(4):274-280
39. Nguyen T.T., Matsui M., Eto K., Mitochondrial phylogeny of an Asian tree frog genus Theloderma (Anura: Rhacophoridae), Molecular Phylogenetics and Evolution, 2015, 85:59-67.
40. Takeuchi H., Savitzky A.H., Ding L., Silva A.D., Das I., Nguyen T.T., Tsai T.S., Jono T., Zhu G.X., Mahaulpatha D., Tang Y., Mori A., Evolution of nuchal glands, unusual defensive organs of Asian natricine snakes (Serpentes: Colubridae), inferred from a molecular phylogeny, Ecology and Evolution. 2018, p.1-14.
41. Nguyễn Thị Thắm, Ngô Thị Hạnh, Nguyễn Quảng Trường, Thomas Ziegler, Mona Van Schingen, Nguyễn Thị Hồng Vân, Lê Đức Minh, Sử dụng chỉ thị Microsatellite trong nghiên cứu quần thể loài thằn lằn cá sấu (Shinisaurus crocodilurus Ahl, 1930) tại Việt Nam, Tạp chí Khoa học ĐHQGHN: Các Khoa học Trái đất và Môi trường, 2017, 33(1S):100-108.
42. Wei X.X., Yang Z.Y., Li Y., Wang X.Q., Molecular phylogeny and biogeography of Pseudotsuga (Pinaceae): Insights into the floristic relationship between Taiwan and its adjacent areas, Molecular Phylogenetics and Evolution, 2010, 55:776-785.
43. Tamaki S., Isoda K., Takahashi M., Yamada Y., Yamashita Y., Genetic structure and diversity in relation to the recently reduced population size of the rare conifer, Pseudotsuga japonica, endemic to Japan, Conservation Genetics, 2018, 19(5):1243-1255
44. Castelán P.M., Cruz M.C., Castillo M.C.M., Izquierdo S.C., Upton J.L., Padilla IS., Cruz V.G., Diversity and genetic structure inferred with microsatellites in natural populations of Pseudotsuga menziesii (Mirb.) Franco (Pinaceae) in the central region of Mexico, Forests, 2019, 10:101.
45. Ho C.S., Shih H.C., Liu H.Y., Chiu S.T., Chen M.H., Ju L.P., KoY.Z., Shih Y.S., Chen C.T., Hsu T.W., Chiang Y.C., Development and characterization of 16 polymorphic microsatellite markers from Taiwan cow-tail fir, Keteleeria davidiana var. formosana (Pinaceae) and cross-species amplification in other Keteleeria taxa, BMC Research Notes, 2014, 7:255.